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ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures
BACKGROUND: Periodic proteins, characterized by the presence of multiple repeats of short motifs, form an interesting and seldom-studied group. Due to often extreme divergence in sequence, detection and analysis of such motifs is performed more reliably on the structural level. Yet, few algorithms h...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4021314/ https://www.ncbi.nlm.nih.gov/pubmed/24766872 http://dx.doi.org/10.1186/1471-2105-15-119 |
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author | Hrabe, Thomas Godzik, Adam |
author_facet | Hrabe, Thomas Godzik, Adam |
author_sort | Hrabe, Thomas |
collection | PubMed |
description | BACKGROUND: Periodic proteins, characterized by the presence of multiple repeats of short motifs, form an interesting and seldom-studied group. Due to often extreme divergence in sequence, detection and analysis of such motifs is performed more reliably on the structural level. Yet, few algorithms have been developed for the detection and analysis of structures of periodic proteins. RESULTS: ConSole recognizes modularity in protein contact maps, allowing for precise identification of repeats in solenoid protein structures, an important subgroup of periodic proteins. Tests on benchmarks show that ConSole has higher recognition accuracy as compared to Raphael, the only other publicly available solenoid structure detection tool. As a next step of ConSole analysis, we show how detection of solenoid repeats in structures can be used to improve sequence recognition of these motifs and to detect subtle irregularities of repeat lengths in three solenoid protein families. CONCLUSIONS: The ConSole algorithm provides a fast and accurate tool to recognize solenoid protein structures as a whole and to identify individual solenoid repeat units from a structure. ConSole is available as a web-based, interactive server and is available for download at http://console.sanfordburnham.org. |
format | Online Article Text |
id | pubmed-4021314 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-40213142014-05-28 ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures Hrabe, Thomas Godzik, Adam BMC Bioinformatics Methodology Article BACKGROUND: Periodic proteins, characterized by the presence of multiple repeats of short motifs, form an interesting and seldom-studied group. Due to often extreme divergence in sequence, detection and analysis of such motifs is performed more reliably on the structural level. Yet, few algorithms have been developed for the detection and analysis of structures of periodic proteins. RESULTS: ConSole recognizes modularity in protein contact maps, allowing for precise identification of repeats in solenoid protein structures, an important subgroup of periodic proteins. Tests on benchmarks show that ConSole has higher recognition accuracy as compared to Raphael, the only other publicly available solenoid structure detection tool. As a next step of ConSole analysis, we show how detection of solenoid repeats in structures can be used to improve sequence recognition of these motifs and to detect subtle irregularities of repeat lengths in three solenoid protein families. CONCLUSIONS: The ConSole algorithm provides a fast and accurate tool to recognize solenoid protein structures as a whole and to identify individual solenoid repeat units from a structure. ConSole is available as a web-based, interactive server and is available for download at http://console.sanfordburnham.org. BioMed Central 2014-04-27 /pmc/articles/PMC4021314/ /pubmed/24766872 http://dx.doi.org/10.1186/1471-2105-15-119 Text en Copyright © 2014 Hrabe and Godzik; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Methodology Article Hrabe, Thomas Godzik, Adam ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures |
title | ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures |
title_full | ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures |
title_fullStr | ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures |
title_full_unstemmed | ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures |
title_short | ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures |
title_sort | console: using modularity of contact maps to locate solenoid domains in protein structures |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4021314/ https://www.ncbi.nlm.nih.gov/pubmed/24766872 http://dx.doi.org/10.1186/1471-2105-15-119 |
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